Subtitles are not a "basic thing". There's several formats of subtitles and even multiple ways to associate them with a video file. Some formats are embedded and others are sidecar files. Different file containers have different limitations on the subtitle formats they support. Just because a subtitle is ostensibly "text" doesn't automatically make them basic.
I am aware that subtitles aren’t “merely text” and that different container formats constrain the subtitle format and number of tracks and so on. Still, this is simple compared to much of the stuff we use software for. Complexity abounds everywhere and yet lots of software manages to bring order to the chaos. There’s no reason this shouldn’t also apply to subtitles.
A trivial example is to try to convert the subtitles rather than defaulting to no subtitles (Handbrake). Another trivial improvement would be warning that the subtitles can’t be brought over to the container format before the 20 hour transcode rather than letting users find out after that their subtitles weren’t converted.